Hello, I am trying to use simpleaffy to generate some QC information. When I load simpleaffy I am getting this error: Warning messages: 1: found methods to import for function ‘as.list’ but not the generic itself 2: found methods to import for function ‘eapply’ but not the generic itself > Also if I proceed with the processing, following the exact procedure in "QC and Affymetrix data", by Wilson et. al., (except substituting my data and an alternative covdesc file) I get no output with ampli.eset <- call.exprs(ampli.data,"mas5"). Perhaps they are related? here is the entire output. R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(simpleaffy) Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following object(s) are masked from ‘package:stats’: xtabs The following object(s) are masked from ‘package:base’: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: affy Loading required package: genefilter Loading required package: gcrma No methods found in "Biobase" for requests: geneNames Warning messages: 1: found methods to import for function ‘as.list’ but not the generic itself 2: found methods to import for function ‘eapply’ but not the generic itself > > getwd() [1] "/home/gserver/GSE4182/test" > ampli.data <- read.affy("covdesc") > ampli.data Loading required package: AnnotationDbi AffyBatch object size of arrays=1164x1164 features (18 kb) cdf=HG-U133_Plus_2 (54675 affyids) number of samples=2 number of genes=54675 annotation=hgu133plus2 notes= > > ampli.eset <- call.exprs(ampli.data, "mas5") > ampli.eset ExpressionSet (storageMode: lockedEnvironment) assayData: 54675 features, 2 samples element names: exprs protocolData: none phenoData sampleNames: GSM94597.CEL GSM94598.CEL varLabels: sample SampleName Group varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' Annotation: hgu133plus2 > names(ampli.eset@description@preprocessing) Error: no slot of name "description" for this object of class "ExpressionSet" > names(ampli.eset@preprocessing) Error: no slot of name "preprocessing" for this object of class "ExpressionSet" > ampli.eset@preprocessing@preprocessing$sfs Error: no slot of name "preprocessing" for this object of class "ExpressionSet" > Also if I proceed with the processing, following the exact procedure in "QC and Affymetrix data", by Wilson et. al., (except substituting my data and an alternative covdesc file) I get no output with ampli.eset <- call.exprs(ampli.data,"mas5"). Any advice on how to proceed would be greatly appreciated! Thanks! Sincerely, Matt Matthew E. Thornton Laboratory Technician III Broad Center for Stem Cell and Regenerative Medicine University of Southern California 1501 San Pablo St. ZNI Los Angeles, CA 90089-2821 ph.:323-442-1688 fx.:323-442-4040 matthew.thornton@med.usc.edu [[alternative HTML version deleted]]